It's been discussed elsewhere that tracking packages deeply enough to
differentiate between locally installed ones and crufty ones is quite
tricky, and should be done later.

I spoke to Lars and suggested that in the short term (probably as a SRU
after release) there be a whitelist of commonly installed third party
packages. Lars suggested that there be a conf.d, which I think is a
great idea. This will allow him to supply a list of commonly installed
packages, but will also make it really easy for people to add their own,
so you'll be able to stop the cleanup tool from removing your favourite
third party software.

-- 
System cleaner removes explicitly installed third-party packages
https://bugs.launchpad.net/bugs/285746
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